Try to eliminate sources of the problem one at a time.
1) Skimmer - you said you already turned it off and still had bubbles. Make sure it's off for at least 30 mins (60 is better) before you declare "I Still Have Bubbles :angry"
2) Turn off the pump to the fuge and see if they go away
3) Get a large (long) tub as a test sump. Put the drain from the tank at one end, the pump at the opposite, and some filter floss between the two. If bubbles are trapped in the water from your return, this should reduce them.

If none of these decrease bubbles, you either have air being sucked into a water line, or the pump's impeller is cavetating