Karlin (part of Prague 8) and Zizkov (Part of Prague 3, neighboring city center). Zizkov feels more "Prague-y", Karlin has same architecture, but also quick access to lot of new office buildings ("Rohanske nabrezi") and is near Vltava.
Both have excellent subway access, you will be in city center <7 min. If you prefer more campus-like feeling, Prague 6 (Dejvice) has large technical campus with lot of young people. Also, city center <10 min by subway access.
Hope that helps!