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The units for torque, as you stated, are Newton-meters. Although this is algebraically the same units as Joules, Joules are generally not appropriate units for torque.
Someone pointed out that Torque is a vector (defined as a cross product) while Work is a scalar (defined as a dot product). However, that can't be the (only) reason for different units. Units are defined for magnitude of a vector, which by itself is a scalar.