I plan to use my GI Bill to complete my Masters degree while still serving on active duty. Will I still receive the book stipend?

I would advise against using any of your GI Bill while on active duty. The moment you tap into your GI Bill you will become ineligible for the Yellow Ribbon scholarship. Even if you don't intend to go higher than the Masters you are working on, it would be better to transfer the whole thing to a dependent who could use the Yellow Ribbon Scholarship. The Yellow Ribbon Program can be worth up to an additional $24k of tuition and fees.

I'd use TA. You get screwed out of BAH is you use I think now. Your op tempo will outrun the TA cap.

Have you considered using TA and save your GI Bill for later use?