There are a lot of references to Raiden undertaking VR training.
One interesting point is that if you play the Tanker mission you get the following conversation in the opening to the Plant:
Colonel: Just a precaution. You are now designated "Raiden." All right, Raiden. You've already covered infiltration in VR Training.
Raiden: I've completed three hundred missions in VR. I feel like some kind of legendary mercenary...
However if you do not play the Tanker you don't get this line.
There is also a conversation between Snake and Raiden that states:
Raiden: I've gone through VR training of the Tanker mission before.
Snake: Yeah? Well I doubt it accurately simulates the events of that
There are other mentions of VR training, but not specifically the Tanker mission in the game. These seem to be referring to the differences between MGS1 and MGS2's controls, but referring to the MGS1 controls as "VR Training":
Colonel: Unlike in VR training, you can use your gun from Intrusion View in the field. Keep that in mind.
Snake: The PSG1's controls have been slightly modified from what you learned in the VR training. Note the differences: [...] The PSG1 can be aimed from upright, crouch, and prone positions.
However nothing is explicitly said to state that MGS1 or the Tanker are VR, just these hints.
An interesting thing is that one game in the MGS universe (although not canon) does have a heavy hint at being a VR mission for Raiden, and that is Metal Gear: Ghost Babel (Metal Gear Solid for Game Boy outside of Japan). During Ghost Babel you play as Snake, however after completeing the Special Mode you get the line:
Commander 'No. 4': Your training is complete. Well done. Your combat capability is now undoubtedly beyond that of Solid Snake at the time of Galuade's fall. Your time is about to come. Get some rest for now .... Jack.
Raiden's real name being Jack and the game not making canonical sense hints heavily that this is Raiden doing VR.
Ghost Babel was also released the year before MGS2, so was probably made this way as a set up to MGS2, and MGS2's development would clearly impact the development team of Ghost Babel.