traveling with 2 year old son. any kids friendly suggestions during stay? (mid Sep)

first international trip with my 2yo son (3 of us)

(surviving on the plane will be a whole another story.. lol)

we will stay in shinjuku (a bit off Kabukicho, near 3 chome station)

Shinjuku~ shibuya ~ daikanyama ~ nakameguro

Tokyo Tower

Asakusa ~ Ueno ~ Akihabara ~ skytree

Ginja

Ikebukuro

etc

these are our tentative places to go to..

any recommendations where it will be good to bring my son?

also, how was your experience with restaurants when you had a stroller? thanks!