All of which are heavily based on open source software, donations, and in the case of wikipedia, user generated and moderated content.

The solution is not centralization. It's decentralization. A decentralized internet archive could not be held accountable, or taken down, by any individual government. It will remain active and fault tolerant as long as enough users keep enough storage allocated to maintain replication and redundancy. One architected with zero knowledge encryption as the backbone (e.g. IPFS + I2P) could even operate within the jurisdiction of hostile governments.