Is there a chance that you'd ever need the thunderbolt port for something else while the VGA display is connected? That's the only reason I'd go for HDMI.
Either way, an anything-to-VGA adapter coming from a beautiful macbook pro is a bit of a bummer.
Thunderbolt is more flexible and can be used for more things, so I'd use up your HDMI to keep your Thunderbolt(s) free in the future. But you do have two Thunderbolt ports, right?