I would recommend to use both. If the journal differentiates "address" and "current address", then:

• "address" is X (where you did the research)
• "current address" is Y (that's where people can reach you now, right?)

If the journal doesn't distinguish them, I would put Y first (it seems to me more important for you). If the journal doesn't allow two affiliations, that the journal is strange; just try to put both affiliations in the one field and see what happens.

I would recommend to use both. If the journal differentiates "address" and "current address", then:

• "address" is X (where you did the research)
• "current address" is Y (that's where people can reach you now, right?)

If the journal doesn't distinguish them, I would put Y first (you seem to consider Y more important). If the journal doesn't allow two affiliations, them the journal is strange; just try to put both affiliations in the one field and see what happens.