It is very difficult to give advice on this question, because to do so reliably challenges your relationship with your son, and it is not my place to do that - and certainly not in a public forum like this.
But
robert7111a has got to the heart of it : how could you ever be "100% certain he is telling the truth" ?
We put teenagers in an impossible situation when we ask for "the truth". They will already have developed powerful senses of 'fairness', 'right', what 'should be allowed' and what 'should not be allowed', but we have immersed them in a world where both the 'serious' global commentary is full of deceits, cover-ups, and the re-description of events with hindsight, and also the entertainment world is full of success following clever deceipts and the avoidance of criticism through saying what others want to hear.
The reason for my little 'lecture' is as a caution before you make the decision on his behalf. More than once I have been in the awful position of assisting a parent who is convinced of their child's innocence only to find after a vigourouse defence, that there was an undisclosed fact or two, which quite clearly put the child in the position which they had been denying so vigourously, and left me feeling unable to give the comfort the parent needed when they realised that they had been drawn into the world that was false, but was the world that the child thought everyone else wanted to hear.
Having got all that out of the way, we can move on to your decision.
If you are beyond any doubt that he was not present at the time and place, then simply respond saying so. The Railways Companies are used to receiving false contact details which are, in fact, the name and address of a 'friend'. They may require a further statement from you both on that point, but it shouldn't be difficult or stressful.
If you do have any doubt that he may have been the person concerned in the incident, then please don't try to deny it - there is probably enough of a Witness Statement by the Inspector to proceed with a Prosecution, though if he is under 18 then that may be less likely to be followed though. This is where you should be trying to reach an Out-of-Court settlement (OOC), by writing in a tone that is apologetic, which identifies the points which he has learned from the incident, and your willingness to compensate the Company for its losses and its trouble in investigating the matter.
Hopefully, you won't mind my little 'lecture' and can now see how the outcomes from the two strategies that I and
robert7111a have proposed could be so terribly wrong for you, if the facts were not as you believed them to be.
Hope this helps.
Regarding this apparent "advice" from
gray1404 :
The onus is on the train company to prove that it was your son who they stopped and questioned, not the other way around.
That is technically quite correct, but knowing that you have already received a letter concerning an incident involving your son (by name and address), then it is poor advice. We can be sure that there is already a Witness Statement bearing those facts which, if neccessary, will be presented as sworn evidence, and has been assessed to be adequatly robust to succeed in Court. In the event that you did let it get to the position that gray1404 proposes (and my advice to you is, very strongly, to avoid that position, just as it would be if I was advising the Railway Company) then it would be a perverse waste of your time, money and stress to attempt a challenge in a Court by putting a Prosecutor's Evidence to proof in front of the Magistrates and others who won't have a clue what really happened, and will just be baffled and annoyed that a matter of mistaken identy was not resolved OOC.
If you are going to make useful progress, then you really must assume that the Railway Company have adequate evidence to convict (whether or not it really was your sone who was involved in the incident).