I was one of the US citizens on the boat when Sirius had his issues with the young stormtrooper/ deputy dog in the shadow of Boldt Castle. It was pathetic and he wasn't the only one who was treated with something less than respect by our "friend" in the customs shack.
I have recently done many crossings between Boldt Castle, Thousand Islands region, Port Huron, Buffalo, and Niagara Falls. The one that searched my car last night was polite about it (although he did ask if it might be easier to bring a compressor along than eleven tanks, LOL) and that was US customs in Port Huron. The last one in PH (US again) gave me the fifth degree about why I had a ton of dive gear for a two day trip to Kingston.
Typically, I find that I can breeze into Canada. Getting back into the US is a more time consuming process and it doesn't seem to matter where I cross.
PS As I understand it, US customs is now making the standard rotations at any crossing shorter so that agents have a little less chance of just waving someone through because they recognize them.