Even when taking Air Canada ... transfers to/from its partners (ie, US Air, United) are fairly seamless, but connections with rivals (Continental, American, Delta) aren't always so smooth.
I fly out of Toronto all the time, most recently two days ago.* For a transfer to the US where both planes are in Terminal 1, I would allow a minimum of 90 minutes unless you have a NEXUS card. (If you don't know what it is, you don't have one.) For transfers between T1 and T3, I'd add an extra half hour for the train. I haven't been to the Ottawa airport in a while, but I'd allow 90 minutes there to preclear as well.
From experience, I can assure you that travel agents in the US are uniformly clueless about anything outside the US, and have trouble imaginining that the situation outside the US is any different from the situation inside the US. Now and then you run into an individual agent who knows about international travel, but they are rare gems, and even if you find one at a big agency like Amex, good like finding him or her the next time you call them.
By the way, did they mention the USDA baggage inspection at the San Juan airport? It can take a while, too. R's, John * - I'm in Dublin now.