Probably go through customs at Pender Harbor
Are you sure you mean Pender Harbour? You would almost be in Powell River by then so I wouldn't cross the straight there.
However, if you are clearing customs on Pender ISLAND then following the Vancouver Island side up makes sense.
The wind will dictate your best crossing.
Many people like to go from Nanaimo up toward Lasquiti Island. You on the straight much longer, but you are on an angle so you may be going into the waves instead of them hitting you broadside. You also have the option of stopping at Lasquiti Island for shelter or lunch. Jededia (between Lasquiti and Texada) is very pretty and worth the visit. You would then follow Texada Island up to Powell River.
You could also cross from Nanaimo and go across to Secret Cove and then follow the coast past Pender Harbour and Jervis Inlet and Grief Point.
The other option and the shortest distance across the straight to cross at Comox. You may end up taking the waves on the beam if the wind is blowing up or down the straight.
Be flexible and check the wind conditions before you make your decision and check to see if Whiskey Gulf is ACTIVE.