For what it's worth, my recommendation would be to use netflow.
ntop supports both fully, but the sflow protocol itself is handicapped (by its design), and netflow is the more common protocol because of that (and as a result has lots of what I would consider better tools).
For more detail you can read this article that TheCleaner pointed you to but the short version is:
- sflow is a packet-based sampling protocol, and is thus prone to sampling error
- netflow works with more vendors' hardware
- netflow has a wider suite of available tools (because it works with more vendors' hardware)
The second and third points would be the most important in my mind -- Netflow being a well-defined and supported standard gives you more options than
ntop when you want to start really diving into your data.