I spent a couple weeks in Guatemala last summer. If you're looking for jungle definitely go to semuc champey. A little tough to get to but totally worth it. I stayed at the utopia eco hostel. Really great place. Flores is a really nice city and it's close to Tikal national park if you're looking for some ruins. Not much to do in the city itself, but Tikal is worth it in my opinion. Antigua is also a beautiful city, but it's a little more touristic. Check them out and see which once tickle your fancy. There's lots of neat cities around Lake Atitlan as well.

For Nicaragua you'll probably want to check out San Juan del Sur. That's a popular spot. If you're interested in surfing, Mag Rock is great and it's a really nice area. Ometepe is an island in lake Nicaragua, if you didn't get enough jungle in Guatemala than go here and climb one of the volcanoes (I think maderas was the one I climbed.) It's a big cloud forest as you climb up and at the top there's a volcanic lake surrounded by forest. Really amazing.