@GoBirds
Both good ages but equally tough b/c I'm sure nap and melt down times are all over the place. Also their heights play into it. Measure the 5 year old and see if he hits any of the height requirements. At 5 my little guy was jacked for the thrill rides, not sure how your's will be. You know them best.
You are in a good resort based on proximity to MK, easy boat ride over with the benefit that on boats you don't need to fold up strollers (like on buses).
Unless they are really into Princesses (no judging

) they you can save a bunch of time by not doing a lot of Princess hunting —unless it's for you, lol. I'm right there man!
Must dos in MK IMO:
• Talking Mickey on Main St
• Mid Day (3pm) parade—Festival of Fantasy. You'll get to see all the main characters and some
pretty spectacular floats. Crowds super dense on Main st, so try and get a spot in Fronteerland. Or, if you are on Main St., my super secret location is right outside the barber shop right at the parade exit (across the street from the firehouse). Its a hidden little nook that not many people see and being it is right before the performers exit, you are more likely to get a high-five from them then anywhere else on the parade. Show excitement and wave the baby around..they love that.
• Philharmagic in Fantasyland. No need for a FastPass, big theater and very low wait times.
• Otherwise, attraction-wise. you cant go wrong with the classics for the whole family: Jungle Cruise, Peter Pan, Small World, Dumbo, etc.
• If you are up for spending a little extra $ on things:
—Pirate's League: They will give your boys a
pirate makeover...bandannas, eye patches and fake beards. heck even
me and the wife get in on it. Gotta make a reservation.
—Wishes Dessert Party. i'm a big fan of these b/c it gets you off main st and out of the crowd waiting for the fireworks. You gotta do the fireworks, but why not do it with a buffet of desserts in front of you and no kids hanging on you or screaming for balloons or ice cream.
Epcot:
• Turtle Talk with Crush. Kids will eat this up.
• Club Cool: free samples of soda from all over the world. Go b/c its rare to get anything free in WDW
• Other then that, Epcot is a tough one with kids that age. If they can get on Test Track then by all means do it. Soarin is great too, but height may be an issue. If they re slightly into Frozen, then that ride is cute, but not worth the wait or FP if they are not.
Lots of character meeting spots within the countries. If you think the kids don't mind going around World Showcase, there is a lot of stuff to see—cultural shows and performers—and things for the parents—lots of good drink and food sampling options.
Studios:
• If they are into Star Wars then this is the pace to be.
• Check the ages, but the Jedi Training is the cool thing here. Gotta sign up super early—like at rope drop—but kids get to fight a 'real' Darth Vader, or other villain.
• Launch Bay has all the SW's props plus Chewie and Kylo Ren
• Star Tours if they are tall enough.
• If they are into Disney jr, then try and get a table at Hollywood and vine. Its a Disney Jr character meal...Jake, Sophia, Doc McStuffins, and Oso (he may be on his way out).
• Def hit the Disney Jr show, the 3 yr old will be all over this.
• Indy stunt show is good for them too.
• Get a FP for Toy Story Midway. Great ride.
Animal Kingdom.
• Its tough, but try and find time for both Loin King and Nemo Show. Nemo show is pretty long, but the props are amazing. If only time for 1, then hit the Lion King show—Shorter and audience participation. Really great show.
• Tough to be a bug can be scary....good show but be warned. You may want to YouTube it 1st.
• Safari, Safari, Safari...thats why you are there. Try and go early in the AM
• The 5 yr old might enjoy the Wilderness Explorers stations. You get a free book at the main bridge into Discovery Island, and all through the park there are stations where they can learn things and get a sticker for the book. Its free and educational...gasp!!!
• Flights of Wonder is a fun show and good chance to sit down
• Rafiki's Planet Watch is a nice place, but a little out of the way. Tough to get to if you don't have a lot of time.
Other stuff:
• Character meals—I'm a big fan. You gotta eat and you gotta see characters...do both at the same time. You can eliminate the Princess ones and stick to the ones with the main characters. Chef Mickey's is real close to you (Contemporary), Tusker house is in AK and Cape May is over by Epcot (Beach Club). You'll get your Mickey, Goofy and Donald fix in any of those. Crystal Palace in MK is Pooh group. And my fav is 1900 Park Fare for breakfast at the Grand Flo, great food and more unique characters—Tigger, Alice, Mary Poppins, Mad Hatter.
• A Take off of the dessert party is the Pirates and Pals Wishes Cruise. Again, extra $$, but you get a dessert party at the Contemp Resort (right by you), meet Capt hook and Smee, then go out on a boat into the middle of the lake with a Pirate skipper (who tells kid jokes and trivia) to watch the MK fireworks (with the music). Then you meet Peter Pan on the way back. Again, i'm all about getting away from crowds, but I normally go in summer time.
Hope that helps, let me know if you have any other Questions.