I received a W-2 from my university when I was a graduate assistant, but my understanding is the position was a stipend and was not taxable income. Are stipends taxable?

The IRS treats as compensation any amount properly shown in Box 1 of Form W-2. This needs to be entered as a W-2. See IRS Publication 590-A for more information.

Stipends are taxable, even if not reported on a W-2.  But it's a common  misunderstanding thinking they're not, because there is frequently no tax form (W-2 or 1099) issued.  It would be taxable even without  a W-2 or 1099. 

Wages and stipends paid to a student by their university are not subject to FICA (social security and medicare) tax.  Boxes 4& 6, on the W-2 should be blank (or 0).