It's awesome that your nephew's family is supportive! Really, that's the key for kids- whether they are LBGTQ or are just otherwise 'different'. If the immediate family ultimately has your back, problems such as peer rejection and isolation become easier to handle. That's not to say they are easy, but that family support goes a long way.
Find out what the kid's interests are and support them- whether they are martial arts, soccer, science, or ballet. Also, make sure he knows he can always go to you with any of his problems at any time.
Finally, make sure he knows about the Trevor Project. The website is
http://www.thetrevorproject.org/ and they have many programs to support LGBTQ youth. Not only do they have phone numbers kids in crisis can call, they also have chat and text-message support programs where kids can find support from a trained adult. Finally, they have a closed, moderated social network where LGBTQ teens can communicate with one another. Even if he doesn't need their support now, he might later.
Best of luck and keep us updated!