Say you have a 1024-bit key. With two primes, each is about 512 bits; with three primes, each is about 341 bits. Current factorization methods require exponential time, so each additional bit requires about double the time to find the factor. Thus, two primes are substantially stronger than three primes.
To be specific, a 768-bit key has been factored, and reported in the mathematical literature, which means that a 341-bit factor can be found (the 768-bit factorization took about 2000 PC-years, so it's not easy, but possible). No one has yet reported factorization of a 1024-bit key (although there are doubtless people working on it).