Chances are, if there is a boat, it will take a motorcycle; preferably small motorcycle. Large motorcycles are not common, so if you may be charged extra for a big bike. Getting a large bike on and off a boat can be easy if the deck lines up with the dock. A wooden plank will do the trick. You may have to tip a few dock workers if lifting your bike a significant height is required. The tip is usually some small amount, but I suggest setting the amount in advance. Try to work with one person when negotiating and let him pick helpers. One loud mouth dock hand and you can be held hostage. Ignore pushy louts and lock in with a sensible helper...

>"...Hey guys, looking to travel to Iquitos from Peru and then from there take and other boat to Ecuador."

Iquitos is in Peru, so your post is a bit confusing. Sounds like you are trying to go from Iquitos (Peru) by boat to Ecuador, right?

See this blog posting from two backpackers that took a boat trip on the river that I think you want to travel:
Travel Blog - Two Bein' Chili

Information on boats is hard to source directly on the Internet, I've tried, I've been frustrated, I've failed. I speaking about schedules and rates. Sometimes you can find info on forum, but it's usually old details. My focus has been on barges downstream on the Amazon. Your mileage may vary.

Keep searching the Internet and mention the river towns where you want to start and end. Add "motorcycle" and see if you can find specific web pages. It's out there if you look hard enough; you will find someone who has been there already.

__________________
Peter B
2008/09 - NJ to Costa Rica and back to NJ
2012/13 - NJ to Northern Argentina, Jamaica, Cuba and back to NJ
2023 - Peru, Brazil, Paraguay, Argentina, Chile, Bolivia...back to Peru.

Blogs: Peter's Ride