The trick with the Manly ferry is to catch it over to Manly from Circular Quay in the mid-late afternoon, wander around Manly a bit (grab some fish & chips, sit on the sea wall and watch the late afternoon surfers and runners/walkers, and finish off with a gelato on your way back to the ferry), and time the return trip so that the sun is setting as you leave. Sit up the front, and watch darkness fall over the harbour and the city light up. Best view you'll get for minimum dollars.
On the other hand, if $$ are not too much of a worry, do the bridge climb. Dusk is the best time there too for much the same reasons, but it's also the most expensive and most booked out.