Last time I cleared there, you pulled up to the customs dock which is on the way in to the inner harbor to starboard, and used the phone on the dock to report. It was quick and I was cleared in on the phone call. This year clearing in elsewhere, you were heavily encouraged to use the Arrive app. We did, but we were asked to wait for an agent, who went through the boat looking in every locker. Took more than a hour.
When you call them, make sure you have the passport numbers for every person, and the boat registration numbers in hand. Also have a notebook to write down the clearance number they will read to you. You are supposed to post that in a visible place, say the window next to the pilot house door.
You will be asked about liquor, food (mainly things with seeds), cash, cannabis and weapons. Not a good idea to bend the truth here, they may come look and Canadian customs agents, like customs agents everywhere, have little sense of humor.