We are also doing that trip and it has been recommended to do the boat tour at Many Glacier not Lake McDonald.
St. Mary boat tour also gets good reviews. I think it is a longer tour than at Many Glacier.
You're not missing anything spectacular on the Lake McDonald boat ride. I think the St Mary and Many Glacier boat rides are both better than the Lake McDonald one for scenery. If you want to see a bit of Lake McDonald area for a few hours, maybe a short hike near the lake or getting up to the Avalanche Lake hike would be a better use of a few hours. IMO the east side and GTTSR just has more spectacular scenery in general. Wonderful scenery and short hikes at Logan Pass on GTTSR at Hidden lake Overlook or you can hike Highline Trail as long as you like and just turn around when you're done. Both are breathtaking and you'll pass right by Logan Pass on the GTTSR. Beautiful photo ops at St Mary Lake which is on your way too.
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