Hmmmm, this is a tough one. On the one hand, all of my favourite Dream Theater albums and songs are from their 90's output. On the other hand, though, I can think of a couple of bands that I like that had decades that rival DT's 90's run, namely:
90's Savatage: Streets, Edge Of Thorns, Handful Of Rain, Dead Winter Dead, Wake Of Magellan
80's Queensryche: s/tEP, The Warning, Rage For Order, Operation: Mindcrime
I&W/Awake/ACOS/FII/SFAM is more or less equal in my mind to QR's EP/Warning/RFO/O:M, and that Savatage run of Streets/EOT/HOR/DWD/TWOM is just absolutely godly.
So no, DT does not have the best decade of music IMO. Definitely in the top three, but I think Savatage wins this one for me, with DT and QR being tied for second.