Peter-
For years, I simply disconnected the ground cables and stored the fully charged batteries on the boat with no issues. I think the preferred approach is to disconnect the positives, but our boat has a lot of cables feeding into the positive terminals, so disconnecting the negative terminals is easier. If they are wet batteries (sulfuric acid) the cells should also be topped off with distilled water.

I have 3 Lithium Batteries, I have routinely removed the batteries and stored in my garage with a battery keeper they are super light, however this year because I am a bit more lazy or maybe older, I left them in the boat with the battery keeper plugged in.  I hope they do ok, concerned about the cold degrading the battery.  My engine battery (lead\acid) is ready to be replaced, will deal with that in the spring.  Another reason to retire down south and\or in the Bahama's so I do not have to take the boat out of the water every year.   Leave it commission all year!

I'm lucky as I'm in indoor heated  storage.  I do use individual trickle chargers for my five AGM batteries.  But back to the basic question.  I do and would disconnect both positive and negative terminals, thus isolating each battery individually.  To insure the wiring is not confused in the spring.  I place colored tape on each battery and their mating cables.  For instance the house bank has blue tape on battery and both the red positive cable and black negative cable, the auxiliary bank has green tape, and the starting battery has white tape.  Each battery is isolated from each other and the whole system is without current.  The chargers are on power strip with a circuit breaker, if one battery shorts out all of the batteries powered down.  Belt and suspenders, I know.  

Lithium Iron Phosphate (LifePo4) batteries can be damaged by charging at cold temperatures. Many batteries have built in heaters to enable use in low temperatures. Partially charged, not connected to a charger or battery keeper and  disconnected from use they should be fine over the winter. 
There is a lot of info available online, best to check the particular batteries you have with the manufacturer.
My solution to avoid charging in cold weather is to move south, trying to keep the boat in at least 70 degree weather at all times.

Attached is the setup for three batteries in front of the nav.station, Aux and Starting batteries.  I'll send another post with the House batteries.

The other two batteries are in the space below the outboard dinette set.  I can't send the photo it is too large for the website.

Lou, great job strapping them in tight.   I have 2 100AH in the same location, and one single 200 ah in the bow on a cradle I glassed in. in the box making a total 400 AH of Lithium and 1 dedicated by the engine where the old water muffler was.  
BRAZEN thanks for your advice, I researched and will unplug considering the cold weather heading our way,