Croatia late November (Thanksgiving)?

If you can get a good flight, I see no reason not to go in November. It will just be a different type of trip. Zagreb and Split (and even Dubrovnik) are large enough to not have an appreciable difference in the off season. I don't like two-day itineraries (I'd be more inclined to spend a week in one of the cities), but if you're cool with that pace, then I would just make a list of what you would want to see in each place and make sure you've given yourself enough time.
I've seen photos of Plitvice in winter and I think it would be great to see it without the crowds.

Here's something if you're a film buff, it could also affect hotels in Zagreb: https://zff.hr/en/

The Holiday season for Zagreb Advent Markets and events start on 30 Nov 2021 until the 1st week of Jan 2022. If Covid permits: It looks great from previous years. Dubrovnik is where they filmed some of GOT. Their Markets start on November 29th. Lots of traditional crafts. Splits Market is on a Seafront Promenade. Looks like a fun week, if things are open.

My trip to Zagreb and Dubrovnik were shortly after Thanksgiving and it rained in Dubrovnik, but I did enjoy a couple hours of sunshine one morning as I walked the wall. As a matter of fact, there was quite a bit of rain while in Dubrovnik and I slipped and fell on the limestone pavement. Don’t bother with an umbrella because the wind will turn it inside out, even if the umbrella maker says it won’t. Do wear water resistant clothing and a top-of-the-line raincoat with a hood i.e., gore tex.
What I liked about going this time of year is that there were no tourists, just college kids drinking at an internet café and invited me to sit with them, they were fun and smart and knew a tremendous amount about US politics. Everything was still open but without the crowds.

I don't necessarily trust the average-temperature data in Wikipedia's city entries, because the time-period covered usually cuts off in 2010 and I figure a lot has changed since then. However, for what it's worth, it looks like the expected average high and low for Zagreb would be about 44F and 32F, respectively, at the end of November. You should expect, on average, one day of precipitation out of every 3 days--more likely to be rain but snow would be possible. Daily hours of sunshine would average about 2.

I like Zagreb a lot but that's not the sort of weather I like to vacation in. However, the city has a lot of interesting museums, so there will be indoor activities available if you need them.

Just an FYI, we are in Zagreb now and many museums in the lower town are closed due to the prior earthquake. Check each website.