Amsterdam to Germany To Switzerland To France by Train and boat

How many nights are you spending in Europe and how long do you envision staying in Amsterdam, Dusseldorf, Basel? Do you wish to stop and stay in the Alps? Take more than one scenic train in Switzerland? Do you fly out of Paris?

Sounds like you are in the initial stages, ideas but nothing fixed. So answers can only be vague.

Train Amsterdam - Düsseldorf and boat (or mix) Düsseldorf - Basel
I would switch that to Cologne (Köln in German) more of a tourist city.

Train through Alps - to where? Presumably you would end up in Italy. Any thoughts on where to visit in Italy?
You need to spend a few days somewhere in the Alps, not just zoom through on a train (or take time on a scenic route).
Consider where and how many days.

travelling to France to fly back to Canada. - Why? Are you intending to spend time somewhere in France (e.g. Paris)?
If so it would be logical to do Paris on the way south, and fly back from Italy.

Suggestions on rail passes... Don't! Except perhaps in Switzerland, if you are staying there and doing a lot of day trips a Swiss Pass of some sort may be worth it. Otherwise buy advance discounted tickets.

hop on hop off cruises..
The most touristed part of the Rhine is the Rhine Gorge Area south of Cologne, from Koblenz to Bingen. There are day boat trips in the section, some starting from Cologne. You could do "Hop on hop off" to the many pretty towns in this section. South of Bingen it is only cruise boats (sleep on board) that do the route through to Basel. You could do that, or take a train, stopping of for example in Strasbourg and other places.

booking in advance or buy once there?
Since they invented the internet, hotels are booked up in advance. You will have little luck turning up in a town and looking for a hotel.
And long distance trains usually have discounts for advance purchase.

All this is vague, but unless you want a complete book "Guide to Planning a European holiday", that is all I can do.

Finally: How many days do you have? Once that is known, you can try and fit "nights in each location", then join up the dots and work out transport.
Your planning has only just begun.

A lot of ground to cover. How many days, how many people, what ages? Luggage volume? Have you read our host's travel hints yet, top left blue menu? How many cities in France? Are you flying to Dusseldorf's big airport, or is that city a major tour objective? (I was there last year, but it was my sixth or so time in Germany.) Are you using bargain air carriers?

Were you imagining sleeping on the Rhine boat, or are you taking a formal river cruise? Were you thinking of the KD line? (Seasonal timetables available for download.) As already noted, an hour or two, cruising DOWNSTREAM (read that again, please) from Bingen to Boppard or nearby is all you need. The rest of the Rhine is mostly industrial Germany. Be sure to use the search box, top center, for "Middle Rhine Valley".

I would not fly Amsterdam to Düsseldorf, or to Cologne. It would be quicker for that distance to take a train.

Planning on 2 week trip,,,,fly and staying in Amsterdam ,,Germany , France,,,visiting Switzerland

Train Travel from Amsterdam to starting point city,,,in Germany to then experience the Rhine for a few hours,by boat ,then hop of boat to continue by train through Germany hop on hop off along the Rhine to Basel,,, staying 3 nights in Amsterdam,,,then 5 days in Germany,,,,2 nights in Switzerland ,,,then visit France and fly out...
Obviously my first trip,,,big dreams,,,looking for expereinced advice ,,, as I embark on this big adventure,,,

Two weeks equals 12 exploring nights. Here's an idea:
Day 2, Land in Amsterdam, 3 nights
Day 5, Train to Cologne, 2 nights, 3 if visiting Duesseldorf
Day 7, Train to Bingen, KD boat to Boppard, sleep in Boppard or St. Goar
Day 8, Train to Basel, 2 nights
Day 10, Train to Paris, 4 nights, daytrip to Versailles or Chambord or Vernon
Day 14, Fly home

Note that this is not an optimal schedule for a first trip to Europe, because you are trying to cover too much ground. But I am responding to your specific requirements for the trip. I personally will not change hotels every day, so perhaps I am the wrong person to give you advice.

Basel is not the Alps, you have to go further south for that.
You said "Then train through Alps" which implies you head south to the Alps - possibly stop s few nights - and then further south through the Alps and end up in Italy.
No way you can do this and still fit in Paris in two weeks.

Adding to Tim's plan, after day 7 you either head for the Alps for 2 nights, then on to Italy (perhaps Venice or Florence) and fly home from there.
Or, give up on the Alps. After day 7, train to either Basel or Strasbourg (and day trip Colmar) for your 2 nights, and from there to Paris and fly home from there.