Colmar to Chamonix by Train

There are no direct trains from Colmar to Chamonix. Two connections are required taking 9h 35m. This link shows a picture of routes in FR and Paris is FRs centric center: https://www.ricksteves.com/travel-tips/transportation/trains/france-rail-passes.

Try cutting through Switzerland. It is 5 connections, but takes anywhere from 7 hours 50 minutes to 6 hours and 50 minutes depending on your departure time.
www.sbb.ch/en

Your bad luck is that the train line between Martigny and Chamonix appears to be shut down for maintenance beginning Sept 29, so you have to go the long way via Geneva and Annemasse.

Rick 's rail maps are famously bad and unrepresentative of fact. The number of non via Paris routes on that map is unreal.
But then I have a proper paper rail map of France and have done a fair bit of travelling on secondary French rail lines.
But it's the same in the UK where he misses off lots of routes, but shows others as direct routes which aren't.
Having said that if you look on SNCF connect for a closer date none of their suggestions sends you via Paris. One is even a Colmar to Lyon direct TGV as the first train.
But on SNCF connect there are too few options for then compared to today, suggesting time tables are not yet finalised.
Breaking down the journey on 30 September Colmar to Geneva, La Roche and St Gervais all work on SNCF connect. It's the last 12 miles from St Gervais which is missing.
That is an hourly train. If there is engineering work there will be bus replacements provided.

Because of the train connections and time, we chose to rent a car in Colmar and drive to Chamonix, spending a couple of nights in Lyon on the way. Took a cab to pick up the car in Colmar (rental place at the edge of town), there was underground parking right across from our apartment rental, turned in the car as soon as we dropped off our stuff at apartment in Chamonix. It was December and had snowed but the road was clear and it was an easy drive. The most annoying thing was there were four of us and we got the smallest car and we were packed in like clowns! But we made it and have a hilarious story to tell.

I am loving this car idea! Can you tell me more about renting in Europe? Is it pretty much like the US? We did rent a car in Scotland once and it was great/easy.

Thank You!

feltes84,
Check Autoeurope for car rental options. They are reliable and we have booked through them often. Also they have good English language customer service support. You can also go directly to the companies (Avis, Sixt, Europcar, Hertz, etc.) Do not rent in one country and drop off in another....LARGE drop-off fee. We have never had a large drop-off fee, if any, with dropping off in another city within the same country. Depending on the cities you go to, there may be some areas that you can't drive in or that need a sticker to drive in. (Like the ZTLs in Italy.)
Get an International Driving Permit (from AAA, about $20.00-$22.00) and make sure your state drivier's license is current. Pay attention to speed limits. France has lots of cameras, and if you are caught, your ticket may arrive a few months later at your home. The rental company will also charge a fee to your credit card for providing your info to the ticketing agency. Should you get a ticket, pay asap as the fine goes up as time passes. Easy to do online.
Remember that the car description may say 4 passengers plus luggage, but the cars may be much smaller than you are used to in the US. (In the past, I have seen a Deux Chevaux described as a 4 person convertible!
We almost always drive and enjoy the freedom a car affords us, but parking in some cities can be difficult to find and expensive as well. Be sure to pay attention to the gas type (diesel or regular) for your car and at the pump! Tapo and pay credit cards have always worked for us at gas stations and toll booths.
Bonne chance!

You will need a Swiss vignette if you go the short way through Switzerland. Cost is 40 CHF.

How does one go about acquiring the Swiss vignette?

I checked and it looks like you can get it at border crossings.

Thanks everyone for the replies! This is really helpful. We love the train, but for this leg of the journey-car it is!!