Does it switch to the Holland Tunnel route at any point in the trip? It's possible that there's a lack of continuity somewhere in the route.

It also could be that Waze doesn't have enough data to know that your route is quicker. This can be achieved by ignoring the instruction and driving it a dozen times. However, if it gets the data and still thinks the other route is shorter, it's still going to keep suggesting the other way. It might suggest it in the other routes if you drive it enough times.

I'll try to troubleshoot it on Livemap and see if there's anything glaringly obvious. There are several area managers around there that will probably do a better job with it than I'll be able to. I'm sure they'll see this post and look into it also.

Ok...found the last two ramps that merge into the final ramp segment before it becomes a Freeway were restricted, going into the tunnel.

Give it a couple of weeks and it should start working.