Yes, Snape's portrait is in the Headmaster's office:
Q: Is Severus Snape’s portrait in the headmaster’s office?
J.K. Rowling: Some have been asking why hasn’t [Snape's] portrait appeared immediately. It doesn’t. The reason is that the perception in the castle itself and everyone who was in the castle, because Snape kept his secret so well was that he abandoned his post. So all the portraits you see in the headmaster’s study are all headmasters and mistresses who died, it’s like British royals. You only get good press if you die in office. Abdication is not acceptable, particularly if you marry and American. I’m kidding! [laughter] I digress. I know, because I thought this one through, because it was very important to me, I know Harry would have insisted that Snape’s portrait was on that wall, right beside Dumbledore’s.
J.K. Rowling at Carnegie Hall -- 20.10.2007 -- Transcript from The Leaky Cauldron