The migration is a difficult thing as more often than not it doesn't do what its supposed to! The big cats fortunately are territorial so they don't follow the migration but instead lie in wait for it to pass through their territory ...... then pounce!
When people think of the migration they think of the wildebeest crossing the mara river but this is in actual fact a quite a rare occurence and can happen anywhere on the river so you'd be lucky to see it. The camera crews on the Big Cat diary etc hang around the river for weeks at a time waiting to see it but having said that many of our clients have been fortunate to be in the right place at the right time ..... one couple saw it 3 times in one trip!
Wether you go to the Mara or the Serengeti in September you're going to see a lot of Wildebeest! The migration stretches for miles and miles so even if you catch the tail end of it it's still going to be spectacular. In light of this I think Tanzania (Serengeti) would be your best bet. In Tanzania there are a couple of "circuits" between national parks that you can do. The northern circuit is the most popular as the parks are quite close to one another so less driving involved. Here is what we normally suggest:-
Fly into Kilimanjaro Airport this is a day flight so you have to stay overnight in Arusha. Drive down to Tarangire NP and spend a couple of days there. It is a really beautiful place with amazing rugged scenery and large herds of ele. From there head up to Lake Manyara and spend 1 maybe 2 nights there. It's beautiful compact wilderness area with a supprisingly large variety of flora and fauna! It is one of my favorite areas in Tanzania and should not be passed through too quickly. Take time to stay at one water source for a while, just relax and watch what passes through. A huge number of species are supported due to the diversity in habitat, within 330 square kilometres (the majority of this is the lake) you will find: the rift valley wall, the ground water forest, acacia woodland, areas of open grassland, the lake shore, swamp and the lake itself ....... truly stunning. It also helps break down the journey up to the Crater.
From here drive up into the Ngorongoro Highlands, past tea plantations and through villages to the gates of the Ngorongoro Conservancy; keep climbing through the rain forest till you reach the rim of the Ngorongoro crater. Two and a half million years ago the Ngorongoro rivalled Mount Kilimanjaro but the cone collapsed and after some time settled to form the crater. Now a days the crater is a combination of Noahs Arch and the Garden of Eden. It is an astonishing self supporting ecosystem sustaining many of the species found in Eastern Africa. The crater is only 20 kilometres wide with walls 600 metres high, it is a stunning spectacle from either the rim or the floor. Having said that I'd only spend 1 maybe 2 days here as it's quite small and it tends to be the preserve of the minibus brigade! On the other hand if you are interested in a bit of walking the Ngorongoro highlands are fantastic and the crater floor provides some of the best photographic opportunities as you can get quite close to the game.
From here you can drive down from the crater passing the Olduvia gorge "the cradle of mankind" where the first hominid fossils were found by Leaky and co. You'll pass the Masai with their cattle who co-exist with the 40,000 head of wildlife in a unique venture of wildlife and pastoralists sharing the land. You'll drive out of the mountains and onto the endless plain, the Serengeti. With 14,763 sq kms this is Tanzanias largest National Park and indisputably one of the finest wildlife areas anywhere in Africa with a huge variety of mammals and nearly 500 bird species. Spend as much time here as you like ..... the game is fantastic and there's plenty of room for everyone, it's the quintessential africa that everyone has in their minds eye ..... wide open grasslands dotted with acacia and large herds of game. Cold G&T/Beer in hand siting on the bonnet of your landrover watching the sunset. This is big sky country.
The northern circuit involves bigger distances and generally we suggest people fly around but if you've got the time drive it. It involves going to some of the largest but more remote and less disturbed parks such as the Selous and Ruaha. With such few visitors (quite hard to reach so people don't bother!) you'll discover this is wild africa! The game in most instances is still quite weary of humans and vehicles and is correspondingly a bit harder to spot (its all there though!) but is truly wild. Walking safaris in both these parks are mind blowing ............. ever stood 30 meters from a pride of lions on a kill? ...... go to Selous. These are some of my favorite parks in Africa as so few people go to them ....... makes you feel like an explorer!
Coast wise you also have a few options Zanzibar and its sister island Pemba are beautiful. Zanzibar can be a bit crowded but has alot to do and see (Stone Town spice markets, scuba diving, ruins etc). Pemba is more laid back a bit more rugged with forest covered hills fewer people but still has white beaches, ruins to visits, great diving etc ........ and 10 different mango varieties! Mafia Island is still blissfully undeveloped and beautiful but apart from watersports etc theres not much to do ..... depends on how active you want to be really!
Hope that gives you some food for thought. If this is your first time to africa than the northern circuit is probably a good introduction ....... save the southern one for next time and the time after that Botswana and then Namibia .... Uganda .....Rwanda .... Malawi .... Kenya ..... Mozambique! Once you get bitten by the bug you'll keep coming back!
P.S. There's an article in the current "Travel Africa" magazine about one of Mr Mears trips/courses to Namibia ....... makes quite good reading.