Definitely carry it in your backpack.
Also, when you go through security, take it out of your backpack and put it in a tray separate from other items. The TSA people will tell you it's fine to leave it in your backpack, but probably 75% of the time they will then want you to unpack and show it to them.
I have the same problem with my LCD projector that I use for presentations. It's certainly permissible to leave those things in the bags - you don't have to remove them like you do a laptop - but you'll save time and aggravation by taking them out.