We've had guests here with kids that age a couple of times so I've probably got more advice than you'd like
Consider a fair amount of meals at home or at obviously kid-friendly places (close to home is always good, pizza joints, Two Boots). It can be stressful for the parents if you try to go anywhere not obviously family-oriented because they will be worrying about the kids (making messes, noise, not finding food they like). Even if they say it's not a problem, they are probably being nice so keep that in mind.
I'd vote Top of the Rock over the Empire State. If they really want to do something different and have a long night, I think Sleep No More is a fun show (not for the faint of heart).
On their last visit, the kids most liked the 9th St playground. We took them to the Bronx Zoo, Propsect Park Zoo (this is best for kids because it is designed for kids with many interactive parts), and the aquarium and the playground was always their favorite. The adults weren't super adventurous so they liked quiet things like the BBG and places where the kids were entertained. The carousel by the Prospect Park Zoo was also a hit. I love the CP Zoo, but if you're doing it for the kids PP zoo or the aquarium are better.
A boat ride can also be fun--the Staten Island Ferry is good because it's free or for a longer, better ride, Circle Line boats have been a hit with our family. I've not done the Shark but it's similar and is good if the kids like fast things.
You should ask them if there are any types of food they really want to try or maybe send them links to menus of some of your favorite places to get an idea of where they might want to go sans kids. Some of family members really loved or favorite neighborhood places, it didn't have to be somewhere fancy.
Also, if they are staying with you, get snacks for the kids. Ask the parents for suggestions but having some juice/milk that they like, fruit, easy mac, and cereal can make life much easier. Buy some little wet naps and packages of peanut butter crackers to stick in your bag when y'all go out to places--you are unlikely to regret having these things. You never know when a hungry meltdown might come and you can save the moment.