I've heard that Cyprus is a nice trip from Israel.
In terms of the places you mentioned and that I've heard anything about:
Milan: I've heard there is not much to do there. That's why we skipped it on our Eurotrip.
Rome: Was great, but it's a city with a lot of history/tours. Not sure how much a kid would be able to handle it. Also, 4 days in Rome even with travel time is more than you'd need. Of course, you can find what to do, but 2 full days is probably all you'd need.
Venice: I'll expand a bit here since so many people are suggesting it. Venice was one of our favorite cities, and we had 4.5 days there. At the end, though, we were kinda ready to go, as we had plenty of time for being bored/walking around. 4 days including travel (not sure if you were including travel or not) is more than you need, but not overkill. I don't think 4 days is nearly enough to do a few cities in Italy, let alone with a kid. Not sure how D93 did it lol. The activities that we thought would take 1/2 days, were shorter than planned, and we spent an entire day at Lido beach, which helped fill up a day, but may not be your thing. Also, if you're going for a Shabbos, Venice should give you the nicest Shabbos of the places I'm listing here that I know about. An important note is that if you're staying at a nice hotel, it will likely be in San Marco Square, which is a GOOD 1/2 hour walk to Shul/Chabad meals. Doable with a kid, but again, something to think about.
Madrid and Barcelona: 4 days is too much IMO for either of these cities alone, but great for both together. It means another flight for you, so again, not sure if you're interested in that.
Amsterdam: We loved Amsterdam, and I would say it's like Venice in terms of 4 days - just a drop too much, but you can keep yourself busy by going to more restaurants and seeing more museums.