How accurate is Google Maps for travel times?

Good, but not perfect. Any planning tool can only give you estimates based on past experience, but predicting the future is by nature fraught with risk. For reasons explained below in detail, Google Maps is currently less accurate for this route in particular and Japan in general than it would be for, say, the SF Bay Area in the US.

As Mark points out, estimated times tend to be "best estimate", which assume you can drive at the legal limit at all times and never take rest breaks. In Japan, driving at the limits is actually more realistic than in many other places, since Japanese speed limits are generally set absurdly low (often 80 km/h even on expressways) and consequently more or less everybody speeds.

On the flip side, at time of writing driving directions in Japan do not incorporate current traffic information, which can be misleading particularly in big cities like Tokyo. Even some of the major expressways, eg. the T?mei between Tokyo and Nagoya, are notorious for traffic jams at peak times/seasons. (Update: Traffic is now accounted for.)

You've also got a whole bunch of ferries in there, whose schedules are not incorporated into the planning, and the big ones (eg. Oma-Hakodate between Honshu and Hokkaido) only run twice a day or so.

I've got to ask, though, are you sure you want to drive this thing from end to end? Tokyo is a nightmare to get around by car, and many of the expressway stretches (eg. Tokyo-Osaka) are both deathly dull and expensive due to heavy tolls. Using Shinkansen bullet trains when possible and only renting a car at your destination if needed is likely to be faster, more comfortable and cheaper if you make use of the JR Pass.

Disclaimer: I work on Maps at Google, although not on driving directions specifically. This answer represents my personal views and not those of Google.

Update since my original lead of "As good as it can be" seems to have sprouted a debate in the comments: all I meant was that Google Maps does a good job of planning, given its inputs. But of course it can't account for your walking speed, or model of car, or the driver's spastic colon that necessitates changing a colostomy bag every 15 minutes, because it's not told about those. Should it? Maybe yes, maybe no. In the aggregate, though, I find it good enough already, and am not aware of meaningfully superior alternatives for general applications.

I've found the estimates pretty accurate in the USA, to the extent that, when I've taken photographs from the passenger seat on road trips, I can often find out exactly where a photograph was taken based on "Seven minutes ago, I took a photo that randomly included mile marker 123; Google maps thinks seven minutes from there takes you to here; Street View matches perfectly." Obviously, that's a pretty short distance but longer journeys seem quite accurate, too.

I cannot answer for Japan, but in Kuwait Google is by no means exact, but it has been fairly close (~5 minutes from my anecdotal calculations) to the actual time it took between destinations.

In Kuwait it also accounts for traffic congestion and will tell you how much delay traffic is causing on your commute. It uses a combination of data points. I know that it uses including cellphone tower data as there was a delay in getting approvals for this and for a while we had maps, routing but no "traffic" information. I am sure it uses multiple data points in aggregate to create an estimate.

In Dubai it has transit information as well, and it has also been very accurate (especially in the wait times between the train stops and the time it takes to walk between stops).

However, it is not the fastest way to get between two points, because it lacks (at least in Kuwait) the ability to re-route based on traffic. So if you know the roads you can always find a faster way. I suspect in Japan it may not know all the best ways to get from A to B.