I am driving from Quebec City to Boston next week, and I typically carry a small backpack in the trunk of my car which contains minimal emergency supplies such as water, blankets, freeze-dried food, and a multitool.

I was wondering if I could get in trouble at customs having this in my car?

You should be fine. I have crossed into the USA and back into Canada many times with more gear then that with no questions asked other then one cursory search by a Canadian border services officer who took a keen interest in some of our gear as she was a hiker herself...

For complete details, the Canada Border Services Agency website has plenty of related info.

I doubt it - I've cross the border at Blaine/Sumas with a multi-tool in my glove compartment many times, they've never keyed on it. Its not like an airplane where you might use it as a weapon to take down a flight crew - you are your own flight crew in a vehicle. Going to Canada they're looking for weapons, drugs, human trafficking, and terrorists mostly; coming back they're looking for drugs, drugs, drugs, bad agricultural decisions, and if you are in a commercial vehicle maybe terrorists and human trafficking. USCBP have dogs, screwdrivers, x-rays and most importantly time to sniff out most of this. Be honest, if they ask about 'weapons' tell them you don't have a weapon but you do have a name brand multi-tool in your emergency supplies in the trunk (assuming it has a blade - if no blade then the tool is just a tool).

That's what I would do, I'm a US citizen; ymmv as a Canadian, but I hope that things haven't devolved so far as to create a different threshold for our friends from the North.

It's not restricted, no need to tell them when they ask if you have anything to declare.

Nope. Not a problem with the multi-tool. Last time over the border, I told them I had a couple of knifves, one in the backpack and one on my person. They asked to see the one on my person, it was a Spyderco Salt-1. When the guard saw it he rolled his eyes, he "pishawed" and obviously knew it wasn't an issue and gave it back to me.

Freee-dried food shouldn't be a problem, just say it is for personal consumption during the trip. Usually, it's the unprocessed fruits, veggies and meats will get you pulled. The only thing that caught me off guard was when I also mentioned I had a personal amount of liquor and they wanted to know if it was Cuban rum (actually it was Captn Morgans).

Hope your blanket isn't loaded with smallpox!