In general, the Spycraft classes, feats, gear, etc. are slightly to moderately more powerful than the D20Modern counterparts. Remember that the their are significant differences in mechnics bewteen the two games.
It's akin to comparing D&D 3E to D20 Star Wars.
Speaking of which... I've found that anything from D&D is very compatible with D20Modern, anything from D20:SW is very compatible with Spycraft (especially if you're going for a MIB type of game), and vehicle rules for D20Modern are almost identical to D20:SW.