I would strain them out. You only want hops during the fermenting process when dryhopping (typically a pale ale) and that typically has a fresh batch of hops for that phase.
Leaving them in only ads more crud in your fermenter. concider the hops spent after the boil is over. Alot of us will boil our hops in a hop bag, so that we can remove them as soon as the boil is over, and not even leave them in until the wort is cooled.