Strongly agree with @StefanZ here, unless there is a particular reason you need to keep Tommy entire it would be much safer and easier for everyone if he was neutered. Then follow with MJ later after she has decided to completely finish with feeding Onyx.
My best wishes for them all to continue to do well and for mum to settle as if she is calling and in heat it is likely she will not eat well which she needs to do right now to feed her kitten and to recover from the pregnancy.
Thank you for all those photographs, they are all beautiful, and Onyx looks suitably cheeky for a 3 week old kitten.
(Do take a look at the thread in my signature as I'd love to see Tommy in there!)