Hi Melissa,
Thanks for visiting the Disney Parks Moms Panel with your question. All of your choices for resorts are wonderful - I really do not think that you can make a wrong decision!
Of the three that you listed, I am going to recommend
Disney's Caribbean Beach Resort with the pirate themed room. I am basing this on the fact that you have two little boys. The Royal Rooms at
Disney's Port Orleans Resort - Riverside are beautiful; however, that theme seems to appeal more to little girls. Likewise, the standard rooms at
Disney's Art of Animation Resort are themed to The Little Mermaid, which tends to appeal more to young girls. If your boys are more into pirates than princesses, I would go with the pirate room at Disney's Caribbean Beach Resort.
One more consideration would be the pools at each resort. While both Disney's Caribbean Beach Resort and Disney's Port Orleans Resort - Riverside have really nice pools, the pools at Disney's Art of Animation Resort are amazing. The Big Blue pool is so much fun and so wonderfully themed. So if the pools matter more to you than the theme of the room, you might choose the standard room at Disney's Art of Animation Resort.
Any way you choose, it will be a great resort. Have a great time planning your trip, Melissa, and please do not hesitate to ask if you have any further questions!