There seems to be two different questions being asked here, the title of the thread: Which ship took the biggest beatings; and the poll question, Which ship had the best defences?
For the former I would say Voyager
, even though the hull always looked immaculate in the next episode and there was never any worries about spare metal to patch up breaches or new conduit piping, etc.
For the latter I would say the Defiant
, as she is small, highly agile, equipped with ablative armour and was primarily designed to fight. Add to that pulse phasers and quantum torpedoes as her armament and she's pretty badass.
Commander Austin Harris, First Officer, Deep Space Nine (by FltCpt. Bossco)
8.01 - Darkest Before Dawn
(Chapter 8 added, 12/09/2015)