Of course the (non-)existence of a black hole is a coordinate-/observer-independent statement (unless we talk only about apparent horizons), but the full energy ("relativistic mass") of a moving object will still show up in the energy-momentum tensor as seen from an outside (non-moving) observer. For instance, if we take a hot gas, we absolutely have to account for its temperature & pressure (the kinetic energy & momentum of its constituents) in the energy-momentum tensor.
To see that this is a necessity, even for a single particle moving at relativistic speeds, consider energy conservation: If you accelerate a particle, you have to expend energy and that energy needs to come from somewhere (say nuclear fission). As a consequence, this energy will already show up in the energy-momentum tensor before acceleration (in the fission case: as rest mass of your isotopes) and, by local energy-momentum conservation (= 4-divergence of the tensor being zero), it then must also show up in the tensor afterwards.
Whether or not that energy can lead to a black hole is a different question. For a single massive object flying at relativistic speeds in an otherwise empty universe: Probably not, because one can simply transform that "relativistic mass" away by switching coordinates, as you say. For several objects moving relative to each other at high speeds, or even a single particle moving relative to the "rest of the universe", it's not so simple, though – you won't find a coordinate system in which all terms in the energy-momentum tensor are small (let alone zero) everywhere.