Considering the prophecy is in direct response to a question about her children it makes a lot more sense for it to be Tommen. It doesn't really gel for her to start talking about Cersei's brothers half way through a sentence.

"The valonqar" translates to "The younger brother/sibling". Read it in context:

"Will the king and I have children?" she asked. "Oh, aye. Six-and-ten for him, and three for you."

Talking about her children.

The old woman was not done with her, however. "Gold shall be their crowns and gold their shrouds," she said. "And when your tears have drowned you, the valonqar shall wrap his hands about your pale white throat and choke the life from you."

Still talking about the children, "their" crowns and "their" shrouds. If you're talking about a group of people and you were to say "The younger sibling", who would you be referring to? She didn't say "your valonqar" but rather "the valonqar", it stands to reason she's talking about the youngest of the children.

Of course as we know prophecy within ASOIAF is not to be taken literally and can be misleading or blatantly wrong, unreliable narrators and all that, but if you're going to take the literal interpretation here it makes a lot more sense for her to be referring to the youngest child/sibling. It doesn't make any sense for her to change subject of the sentence part way though, if we look at what she actually says (within quotes) and substitute in the translation of valonqar:

"Gold shall be their crowns and gold their shrouds, and when your tears have drowned you, the younger brother shall wrap his hands about your pale white throat and choke the life from you."

I used brother because she uses the pronoun "he", but the word could just as easily be "sibling".