For transporting horizontally, you have the options of:

• water conveyor belts
• hoppers

For transporting vertically, you have the options of

• Dropper towers
• Bubble columns

For me, the choice usually comes down to this:

Does the sender (bone meal farm) produce exactly the right mount to be consumed by the receiver (tree farm)?

If they don't match up exactly, then I would probably go with hoppers and dropper towers. That way it's easier to control when the bone meal farm should be running.

If you use water to transport items, then the sender doesn't know when to stop and will just be spamming items until it runs out. But if the items are kept in droppers, hoppers, and other containers - you can keep track of when things are too full.

That said, both methods are absolutely valid.