I'd recommend taking an a sunset cruise, snorkeling cruise etc. All of them take you by the arch and you can get a good look at it. You also usually get drinks/ food included as well.
If you want to get off at lover's beach, then just take a $10 water taxi there from either Medano beach or the marina. There's not much out there so bring your stuff with you. Nothing valuable as it's kinda rough getting in and out of the boat near the beach.