From a security point of view, all the options you mention are adequate, provided they are configured securely. Secure configuration is mostly about key management; the model I'd suggest is that every server has its own private key, and also the public keys of all the servers it needs to talk to.
You need to consider whether you want servers to talk directly to each other, or you want a central hub. SSH and SSL fit the peer-to-peer model naturally. VPNs would generally favour the hub model, but it is possible to have a peer-to-peer VPN, e.g. Freelan.
If you need to secure a variety of protocols then a VPN may be the best option as you can configure the security once, and all the protocols benefit from the VPN security. If it's only one protocol, then I'd favour SSH for administration and file transfers, and SSL for everything else.