I have done it through the Oswego Canal, Champlain route (when the Erie was closed), and have gone up the St Lawrence and done Welland several times (both ways). Know nothing about the Mississippl route other than that it is there.
1. Going down the Welland or the St Lawrence locks is quite easy. You can do it with two people and it is snap with three. Really not a big deal at all.
2. The distance from Whitby (just east of Toronto) to Albany (where the canals end and you can start to think about putting the stick up) is, to the mile, twice as far going the the Champlain route rather than the Erie Canal route. We had to go via the Champlain route because of flooding on the Erie so it is perfectly doable, but I don't see any advantage to it.
Both canal routes are quite pleasant and not too long so you get bored with the motoring. The latter might be an issue if you entered the Erie Canal in Buffalo. We had nice weather for crossing Lake Champlain with the mast down. I imagine that this might be a problem if the weather is unsettled. There is even a nasty, shallow lake on the Erie Canal (Lake Oneida). It is only a couple of miles wide but about 20 miles long and kicks up a nasty, short chop easily. Make sure the mast is very well-secured before you cross it and don't cross if the forecast is not good. Might want to go at first light before the wind comes up.
3. If you go this way you can put your own mast up at the Castleton BC just south of Albany. They have an excellent crane that was $1/ft a few years ago (sometimes they charge by boat length and sometimes by mast length). Best to avoid weekends since the crane site is exposed to wakes. If you are going south for a year or two and coming back you can mark your mast supports and leave them at Castleton for your return. (They may be there)
4. The St Lawrence route gives you access to some spectacular cruising grounds. I cannot recommend the south coast of Newfoundland too highly. Spectacular scenery, whales, friendly people, remoteness - even icebergs if you go a little further. You need to be self-contained going this way. There are not marinas and you have to be careful with fuel
usage in places but it is worth it. It will not be very warm so you need some warm clothes. Radar
is pretty much an essential until you get well into New England. You don't really go near the Bay of Fundy unless you want to, but there are tides (17' at Quebec City as I remember - the marina has a lock entrance) and you will go very fast downstream with the current and tides. Highlights are (in order of when you visit them): Quebec City, Gaspe, Magadlen Islands, Newfoundland, St Pierre (part of France), Bras d'Or Lakes. Maine, and then you catch up with the canal folks in NYC.
If you have any questions let me know.