This method of getting to the Insomniac Museum is one of two ways that Insomniac intended for people to find the museum. The first way is to beat the game with the appropriate level of completion. The second way is to be at the right place at the right time, as described below.
The right place is on the planet Boldan, in the courtyard near the big clock, on the top of the fountain. The right time is 3am by the PS2 clock which should also be 3am as shown on the big clock mentioned above.
So, into the specific details: I suggest you try this after you have unlocked the electric fence and cleared out the enemies in the two courtyards that are to the left once you pass the electric fence. You don't want to get shot while trying this! The fountain that you need to stand on is closest to the clock and it is the only fountain in the immediate vicinity. Don't confuse this with the pair of fountains in the opposite courtyard. To get there from your ship, go through the deactivated electric fence, up the walkway and turn left. Walk to the end, into the room that you opened with the switch that has two stairways leading up and out of it. Take the left stairway and the fountain will be straight ahead of you in the courtyard. There is no water running in the fountain; it is just a stack of what looks like bird fountains of decreasing size. Stand in the center of the transport pad in the top of the fountain when the clock nearby chimes 3 (at 3am) and a message will appear saying ''Press Triangle to go to museum'' or something similar. Press Triangle and you will transport to a hallway with some bad guys. This is the entrance to the museum.
There has been some controversy over how exactly to do this, people having various problems, etc. so I think more detail will be of use. Obviously if your PS2 clock is set right, go there at 3am, duh. I have verified that this works if you are in the center of the transport pad while the clock is chiming 3am. I do not claim that it works any other time outside of the few seconds while the clock is chiming. In fact I went back a few minutes past 3 and the transporter did not work at that time. I also do not claim that this is the only time that works. However, I have personally verified that this works when the PS2 clock is at 3am PST, and many others have corroborated this.
If you do not feel like waiting until 3am, do the following:
Reset PS2 clock to 2:55am and your time zone to PST. Now, load the game and get to the abovementioned fountain before the clock strikes 3. Follow the rest of the directions above. If you need more time set the clock earlier than 2:55.