Nope, amphetamines aren't covered by the current policy (in the majors, anyway - the minor league policy covers a lot more compounds, and might cover amphetamines). The major league policy is pretty much steroid-specific.
I don't think they'd be off-limits for a whole baseball season, major or minor. Many people are on prescription amphetamines for pretty much the same benefits that they give everybody else (hyperfocus, mental stamina, physical energy, increased awareness and alertness). Banning speed would mean that everyone with a prescription would either have to go without for the season or that everyone with a prescription would have to file paperwork with the league bureaucracy. Prescriptions are easy to get, so it wouldn't make much sense except as a PR move to show that they're cracking down on performance-enhancing drugs.
Meth is one thing, but drug tests can't distinguish between the amphetamines (and even pure methamphetamine (Desoxyn) is sometimes prescribed). Steroids, on the other hand, are very rarely prescribed for long-term use, and generally for conditions that would keep someone from playing. Basically, there's a legitimate medicinal use for amps in baseball, but not steroids.
It'd be interesting to see what their speed policy is, though.