This is really difficult because the person(s) with whom you need to have a conversation is Tom's parent(s). As a 14-year-old, Tom may have some idea that he smells but he is not really in a place to do much about that if his parents allow their whole house to stink. Tom might be a good friend of your sons, but before you embark on any course of action I would ask yourself if you know his parents well enough to be able to have this kind of conversation with them.
I am basing my answer on an experience of my own - in 1997 we had a French student come to stay with my family for 2 weeks whilst on work experience in the UK. She smelled terribly of body odour, so bad that she left a trail through the house as she walked. You could actually smell where she had been and estimate the path she took. Obviously, this was due to poor washing of her body, but it was exacerbated by the fact she was not washing her clothes properly either - instead of doing proper laundry or asking for help doing to while staying with us, she had been washing her clothes in the bathroom in nothing but water and then allowing them to drip dry in her room. We addressed this problem by approaching her, not about her own body odour, but about the odour of her clothes in her room. She took this on board rather well and improved all round, and I feel this is because we did not offend her personally by saying she smelled, but logically she came to her own conclusion that her clothes smelled because she did.
Therefore I would suggest you play this smell down in a similar way by addressing it as a "cat odour" on Tom's clothes, rather than go straight in and say "your house stinks of cat urine".
Perhaps the next time you return Tom home you could ask:
Do you mind me asking if you own a cat?
(A little disingenuous if you already know this. If the cat is there when you go or you have seen it on a previous visit you could instead say "I see you own a cat")
Then go on to say:
I noticed that Tom's clothes had a bit of an odour and I was concerned that something had happened, but if you have a cat that explains it.
By saying that Tom's clothes smell and not Tom himself it softens the blow somewhat as you are not saying "your son stinks". Likewise by saying that you were concerned something had happened to him you are showing you care about him and that it might have been an "accident" of some kind. Ultimately though you are planting a seed in their mind that the smell of their cat is noticeable upon their clothes outside of their house. What they then do with that information is really out of your control. If they have some dignity they may well clean up a bit. Unfortunately, though, some people are oblivious to smells and just have no understanding of cleanliness.
Are your sons at school together? If they are then a fallback option might be to mention it to their school, and see if they want to tackle it with Tom's parents.
If you are really concerned that Tom is living in squalor then there may be an authority you can report this to. I know this may not achieve all of your stated goals and is not exactly an interpersonal solution but I would feel remiss not to mention this while giving advice about a child in a possible neglect case.
