Here is a general Trip Advisor list of some of the hotels/motels in the area. I've only stayed in Otter Creek Inn, Bridgeview and camp at Wellesley Island State Park before.
Sorry! But this one has been completely booked by a golf group that weekend!!!
Riveredge
Hotel
This hotel is located right in Alexandria Bay. The cool thing about this hotel is all the room has a view! Depending which type of room you want, the rates vary. Check the website for rates.
This motel is located between Alexandria Bay and Clayton, near the TI Bridge you will need to take to get to the wedding sites.
This is a really clean, but small motel. David and I stayed there the first time we've ever gone up to 1000 Islands and really enjoyed it. However, you usually stay at places like a Courtyard Marriot, I wouldn't recommend this place to you.
This resort is located in Alexandria Bay, right next to Riveredge. Unlike the Riveredge, not all the room has a view. From what I heard, this place is pretty comfortable.
This place has log cabins (the most expenisve) that you can stay if you would like. I've never stayed here before, nor do I know anyone that has, but it is one of the bigger hotels up at the 1000 Islands.
Do you like camping? Would you mind staying in a cabin with bare minimum? If your answer is yes, then this place is for you! This is where the ceremony is.
This Inn is very clean. It's in Alexandria Bay but it's off the beaten path a little, hence the nice prices. David and I stayed there once and we didn't have any problems with it. If you have AAA, it's worth a shot to see if they give you a discount!