Another vote for Hakone SO LONG AS the weather is decent. The open-air sculpture museum is a big open space good for the kids to be running around. Also the faux "pirate ship" may be an appeal (though check the cruise duration). I also won't recommend the bus tour--probably less kids friendly, and Hakone can be navigated fairly easily without guides. I suspect the schools are not out till the latter half of July, things may not be too crowded yet. Kamakura is nice, fairly low-key, the kids may like chasing the pigeons near the hachimangu shrine, or the tram train rides along the beach. I've heard of some kind of man-made beach in Odaiba but never been there myself so can't comment.

For Tokyo I thought of Ghibli museum but your kids would probably a tad too young. Agree with others about teaching your kids "quiet voices". Ryokan meals--they can be quite flexible to accomodate the kids (though probably defeats the whole purpose of going to an exotic ryokan experience only to have the kids eat chicken nuggets and spaghetti bolo, IMHO).

Are you taking just one stroller? Don't even thinking of bringing a double-stroller. Most major terminals (and even some subway stations) now seem to have elevators/escalators.