1st trip for my kids any ideas?

I will be going to Tokyo and Kyoto.

Any recommendations?

For how long are you visiting; what are your (and your kids�f) interests, how old are your kids, just to list a few questions that come up in my mind? :)

Ages? Interests?

Searching around this website can provide you with plenty of ideas, including a whole page about travelling with children: https://www.japan-guide.com/e/e2460.html

There are numerous theme parks and places you can go to. Many take their kids to the 2 Disney parks by Tokyo and USJ in Osaka, but if you fly around the world to see Japan, why not see Japan? There are others you could pick as well, like Edo Wonderland by NIkko, or the Toei Eigamura in Kyoto.
TeamLabs is another idea - Borderless reopens in Tokyo next month, and Planets is still operating at Toyosu in Tokyo. There is another TeamLab exhibit at the Nagai Botanical Garden in Osaka in the evenings.
https://goo.gl/qyQtGV

Fuji-Q HIghland is an amusement park at the Fuji 5 Lakes.
Lots of other possibilities, such as if they like Japanese anime/manga, or the Cup Noodles Museum in Yokohama, etc etc. It's up to their interests. And of course, to just go where they'd like might not make a great trip for you, so balance things out.

It would be better if you shared the ages of your kids as there are plenty of places for kids in Tokyo to go to. Some of these places are Disneyland, Skytree, National Museum of Emerging Science and Innovation and Odaiba.

My kids always liked Nara more than Kyoto, with the deer and Todai-ji, and the generally more "park-ey" atmosphere. Otherwise, each year they would have a different thing to obsess over and they were pretty happy as long as they were getting it scratched frequently. Grape fanta one year, tonkatsu one year, tempura one year, cos play one year, pugs one year.

Totoro/Ghibli is never a waste of time. Possibly school them up with some anime before you go and visit some places from the shows. They get bored with the temple hopping but usually like the shops in the street leading up to them.

Our toddler loved Nara, too. Went over the moon feeding senbei to the deer. Loved the parks in Tokyo as well as there was plenty of space to run around. USJ and Disney were not appreciated much by our toddler but loved by our grade school-aged nephew. So I guess it all boils down to age and interests.