Definitively 4 distinct nucleons. Combinations of more than 4 quarks have never been observed. The existence of tetraquarks is pretty much confirmed [1]: the so-called Z(4430) whose quark content is $c\bar{c}d\bar{u}$. The next-lightest candidate, the pentaquark, has been entertained but the conclusion is currently that it does not exist. So 12 quarks!
Interestingly, note that the tetraquark mentioned above is heavier than an $\alpha$ particule (4.4 vs 3.7 GeV/c$^2$). The putative pentaquark resonances have masses around 4.4 GeV/c$^2$ too. Thus even without all the evidences provided by a century of nuclear physics which point to the fact that $\alpha$ particle are made of nucleons, clearly a dodecaquark would be far too heavy…
[1] https://arxiv.org/abs/1404.1903