Yes, it is taxed for income tax purposes. However I don't think you pay social security or medicare taxes on it. I think you just pay that on the annual training (full pay) money you earn. It has been a few years, but I do recall being taxed on that differently than everything else. I could be mistaken though.
Also , just an FYI, I believe the stipend is fixed at 75% of O1 base pay. So you can look up each year's pay chart and calculate how much you'll make when the new pay scale goes into effect.