Tough question. The best answer depends on where you are on the lake, and whether you know the terrain around you in advance. Do not guess. Do not say, "I think I know a good spot from a couple of years ago that we might get to." It also depends on how experienced your crew is, and whether you've got three people who can handle boats (assuming two ski boats). Minimize the variables and moving parts as much as you can when the chaos is going on. If the storm (mostly the wind) isn't horrible, and the whitecaps are manageable, it may be best to head right into the wind, and ride it out. At least that way you won't hit anything. And won't lose anything. Take your valuables off the tables in the houseboat, store things away safely. Make sure things on the roof are tied down, or taken inside.
The problem with heading to a beach (assuming you know there's one nearby) is that you have three boats to manage, and the wind makes any landing very difficult, if not dangerous. The last thing you want to do is guess and hope there's a landing somewhere, untie your ski boats, watch one drift away in 40 MPH winds, have someone try to swim after it, and then you're in really big trouble. Or maybe you do manage the boats, but an engine dies on the houseboat in all those waves, or you run aground and need help. Or 50 other bad scenarios. For an account of what this might look like, read here:
This is not actually a hike, but the story of the most frightening storm our group ever encountered on Lake Powell... Warm Creek Bay August 20, 2004 Lake Elevation: 3575’ The sunny morning with all that promise slowly gave way to a lazy summer afternoon. The skies to the southwest soon began...
wayneswords.net
You are unlikely to be near a marina when a storm comes out of nowhere, but if you are, that's a lucky possibility of course. Almost as good is simply to find a sheltered cove or wide mouth of a canyon, and stay away from the walls. Waves and wind effects are likely less severe in those places, but of course there are no guarantees. Whatever you do, don't panic, because the storm isn't likely to last at maximum intensity for very long. As I say, rain is not a big deal, it's the wind.
But bottom line is if you have a manageable situation, and things are tied down, you've got everyone aboard, and your ski boats are not posing a threat to the houseboat, keep it simple, stay out of the middle of large bays, head into the wind, keep it slow, and you'll get through it.