The boats and ropeway close down when the weather is bad, which can happen throughout the year.

I think they stay open in winter on a reduced schedule, but Wikitravel says, "Portions of the above circuit may close for a short period of time in the winter for maintenance, but shuttle buses replace the closed services, so this won't ruin your trip."

Actually I think it would ruin the trip a fair amount since the collection of transport is a goodly part of the fun. I'd suggest contacting JNTO to find out when closures are planned.