chore: bump up controller-runtime, tools, client-go and apimachinery version

[cychiang]

Description of your changes

It would be good to keep using the same version as crossplane-runtime so this PR upgraded the following dependencies version:

From sigs.k8s.io/controller-runtime v0.16.0 the SyncPeriod in ctrl.Options has been removed and replaced by cache.Options, so update the code based on this.

Fixes #

I have:

• [x] Read and followed Crossplane's contribution process.
• [x] Run make reviewable to ensure this PR is ready for review.
• [ ] Added backport release-x.y labels to auto-backport this PR if necessary.

How has this code been tested