The following is my personal (i.e., includes all of my mathematical prejudices) ranked list of subject area journals in number theory.
From best to worst:
1) Algebra and Number Theory
2) International Journal of Number Theory
3) Journal de Theorie des Nombres de Bordeaux
4) Journal of Number Theory
5) Acta Arithmetica
6) Integers: The Journal of Combinatorial Number Theory
7) Journal of Integer Sequences
8) JP Journal of Algebra and Number Theory
For a slightly longer list, see
but I don't have any personal experience with the journals listed there but not above.
Moreover, I think 1) is clearly the best (a very good journal), then 2)-5) are of roughly similar quality (all quite solid), then 6) and 7) have some nice papers and also some papers which I find not so interesting, novel and/or correct; I have not seen an interesting paper published in 8).
But I don't think that even 1) is as prestigious as the top subject journals in certain other areas, e.g. JDG or GAFA. There are some other excellent journals which, although not subject area journals, seem to be rather partial to number theory, e.g. Crelle, Math. Annalen, Compositio Math.
Finally, as far as analytic and combinatorial number theory goes, I think 4) and 5) should be reversed. (Were I an analytic number theorist, this would have caused me to rank 5) higher than 4) overall.)