I would build an underground bunker on a planet inhabited by primitive sapient lifeforms and then go into stasis.
Nice idea - and yes, I would hide, too
But I would do it on a Normandy like ship...stealth system and all, only bigger (with lots of genetic samples from all the species (talking about fertilized embryos) as well as databases containing as much of their history, culture (literature, music, art) and knowledge as possible), a self repair-system that has multiple backups, good defenses (if it is found before the sleepers are woken after a few thousand years, when the reapers have left already...that would be checked by sending unmaned probes into systems with relays) and the possibility to go to minimum power levels and life support - possibly using something akin to very powerfull photovoltaik panels)
And after waking I would start up by bringing back the species from before the extinction cycle, start creating a powerfull military, take over the relay network completely (and turning the alpha-relay - the citadel - into a gigantic bomb (after all, wipping out the reapers with a supernova-like explosion seems like a good idea to me) 
greetings LAX