Sept & Oct are peak season both countries, at prices to match.
How many travelers and what kind of budget are you considering? Do you wish a 'group' tour with set-schedule, dates, routing, accommodations? Or wish to travel 'private' where you decide where, for how long, your choices?

Where do you expect to arrive? Nairobi Kenya or Kilimanjaro Tanzania, and then homebound?

As to Vic Falls, this can be difficult at best with only 2/weeks. Besides the limited flight schedules often at strange times, expensive costs, and four-hours flying time and for how many days did you expect to spend here? With flights, extra Visa, etc... usually at mimimum 4/days. And, if you plan to visit VFA, you'll have to consider flying home from southern Africa - Johannesburg/JNB.

This would leave only 10/days for safari and with that it's usually not recommended to visit both Kenya & Tanzania. The migration is taking place in the Masai Mara during Sept and early-Oct. Those herds that do remain in the Serengeti, are at the very north, where there are few camps and those that are tend to be expensive.

You certainly can't, during this peak season wait to book something till you arrive, where what you might want is just not available. There are many reputable tour operators in your home country or in-country outfitters in both Kenya or Tanzania... best to plan ahead of time.

As sandi has put it clearly,this will be the peak period for Kenya and Tanzania.The spectacular annual wildebeest migration will be purely in the Maasai Mara and a camp next to the river can be a perfect choice.I could suggest Sanctuary retreat-Olonana-though a bit expensive.

In two weeks you have enough time to visit Serengeti,Ngorongoro crater and Lake Manyara-all in Tanzania.Ngorongoro farm house-Ngorongoro crater.You will stretch too far to get to Victoria falls.
You should not fear using any outfitter in both sides as the likes of www.speedbirdsafaris.com or Afriland tours for the two countries.
It could be a great risk hoping for a last minute booking during this peak period.
Cheers.

I booked my Safari with a local company in Tanzania/Kenya and it was $1,000.00 cheaper per person than booking the same Safari in my local city....with Safari Tour Specialist.

Thank you for all your responses. I guess I will have to skip Victoria falls. I realize I need to get cracking on planning the trip. thanks again, i am sure i will be back for more questions.

Percy, can you give me the info on the company you used.
I have started figuring out the logistics of my trip. Here are a few problems i have-
1.can i skip the Serengeti since i would cover the same at Masai Mara and since the migration would mostly be in that area.
2. Is one better than the other- Lake Maynara or Tarangire since both seem to have a concentration of elephants.

Amboseli is another option but I dont want to rush the trip by trying to squeeze in too much. I will be flying into Nairobi and flying out of dar es salam. thanks

I went to Tanzania and Kenya last year for 2 weeks in late Sept & early Oct. Tarangire was well worth the visit, so many elephants, but we saw herds of zebra and wildebeest, too. The baobab trees alone are enough to go there. We only spent 1/2 day in Lake Manyara. It has a very different habitat, but you could easily skip it at that time of year.
We went to central Serengeti as well as Masai Mara. Last year, the herds had already moved from the Mara back into Tanzania, so it's iffy to suppose where they will be. Central has a large resident population and the guides generally know about where they are, so you see a lot. In the Mara, we saw more cats than anywhere, and at very close range.
We were able to fly from Serengeti to Mara. It was a join venture between Coastal and Safarilink. Expensive, but saves time and a hotel stay in Nairobi.
Good luck.

Two safari planners I'd recommend for Kenya and Tanzania are Sandi at Africa Serendipity (yep, the same who so graciously shared her knowledge above) and Bill Given of The Wild Source. As noted, Victoria Falls is in southern Africa, so it's not a good fit with East Africa. "A little over 2 weeks" will barely be enough time if you're going to both countries. It's hard to say if the bulk of the Migration herds will be in the Mara or the Serengeti in your time frame. If the rains start early as they did in 2008, the herds could all be back in the Serengeti early... no way to tell in advance.

In case Percy is off on an adventure and does not respond, here is the report.

http://www.fodors.com/community/africa-the-middle-east/out-of-africa-trip-report.cfm

Predators was the company.

September-October in East Africa will be amazing... sandi laid it out very well. I went in late august of last year and the mara was just spectacular... for a tour company i recommend kiliwarrior... you can customize your trip with them and they get you better prices than many companies... but as i have learned over and over, there are many fantastic tour companies that run in east africa... the best recommendation i can make for you is in tanzania. You usually take the same car and driver through the parks in tanzania so i would recommend finding a company that is well known for great guides. We had george from kiliwarriors and he really made the whole experience great. I have done Wildlife Research in Africa and I feel that I know a great deal about the wildlife in africa and george was able to teach me a lot which was amazing. What ever you do, stay away from vic falls... it is beautiful but there isnt much to do there but see the falls and that is only a 3 hr experience