Basically, the input impedance of an antenna, any other resistance or reactance, and characteristic impedances are circuit-level descriptions for handling voltages and currents, while the free space wave impedance is for describing electric and magnetic fields. In particular, the (real-valued) 50 Ω input impedance means if you apply 50 V of voltage at the antenna feed, 1 A current will flow trough the antenna feed point. The free-space impedance has no relation to any antenna or material configuration. It describes the ratio of electric and magnetic fields in a propagating plane wave, which is approximatedapproximatly obtained in an infinite distance to a radiating antenna.
The first impedance mentioned in the question is the input impedance of the antenna, which is a sum of radiation resistance, loss resistance and reactive components which are described as the imaginary part. It is related to currents \$I\$ and voltages \$V\$ at the feeding pont on a circuit-description level, i.e., $$R = \frac{V}{I}\,.$$ Changing the feeding point of the antenna, the value of this radiation resistance might change (this fact is employed e.g. for the matching of inset fed mircostripmicrostrip patch antennas). The radiated fields, however, stay basically the same.
The radiation resistance is not a real resistance, it is just a model for the radiation case (i.e., operating the antenna to transmit power), where power gets lost from the circuit point of view since it is radiated away. (On a related note: using this resistance for the receive case is misleading, since there occurs no loss in the radation resistance. It is still important for matching, though.)
The second impedance is a wave impedance of the fields, which describes the ratios of electric (\$E\$) and magnetic (\$H\$) fields. The free-space impedance, for instance is given as $$ Z_{0,\mathrm{free\,space}} = \frac{E}{H} = \pi 119,9169832\,\Omega\approx377\,\Omega\,.$$ (This exact value was used before 2019, see Wikipedia on the free-space impedance) We can immediately see that fields and voltages have a relation that might change with geometry etc, or there might be no unique definition of voltages (e.g., in a hollow waveguide).