I want to go to East Africa in Sep or Oct this year. I want to go Zanzibar, Ngorongoro crater, Mto Wa Mbu, Serengeti, Arusha, LakeVictoria. All these are Tanzania and I’m wondering if the parks mentioned are good for seeing the big 5 in Sep & Oct or wether I should go into Kenya as well? I believe the annual migration is generally in the Masai Mara, Kenya at this time? How bigger factor is this in seeing animals? Will there still be a reasonable amount of animals in Tanzania?
What would I miss out by not going into Kenya?

How long do you have in total? The places you're going in Tanzania will take you a decent amount of time to cover, so if you don't have a lot of time you may want to stick with Tanzania.
That said, the annual wildebeest migration in the Masai Mara goes from July-September with the wildebeest usually arriving in Kenya in Aug/Sept and leaving in Oct/Nov. Depending on when you time your trip (Sep or Oct) it could be a good time to visit the Mara for the migration. You may miss it if you only go to the Serengeti during that time.