The planet-assault Vasari capship (for the life of me I cannot remember the name right now), the one w/ the missile swarm, is also really good at assaulting starbases. The bonus damage it gets vs structures applies vs star bases, too. Also, the disintegrate ability rapes caps/starbases.
Furthermore, a pair of lev 10 Kortuls can facerape a starbase by themselves given a enough time.
And lastly... the Subverter shield debuff works against star bases... so... that + phase missiles (including bombers) = lol, starbase! You can make it even more hillarious by popping the lev 6 Kortul ability on the starbase (the +30% dmg one). Add the Jarasul's nano disassembler into all of the rest of that... you get the idea.
Be prepared to lose some ships though, unless you use a ton of bombers (alone), or have a couple skirantra's and/or a ton of Overseers repairing your fleet.