Just back from a 6 night stay at the Peponi in Lamu. It was a great experience. Things feel very safe there, and we did some great snorkelling. The hotel is idyllic. It does not leave you feeling like you are in a garrish, over-touristy hotel, but has all the comforts. It is owned by a family (second generation now running it), and while you have your privacy, it can almost feel like staying in the lavish home of a friend. The staff are exceptional: friendly and capable. The location is the best in the region, with lovely winds, a great beach and close to Shela's amenities. We arrived there with no luggage (Kenyan airways doesn't get such a positive review). The hotel worked all work with their contacts to deal with the missing luggage, and the owner even lent us clothing to get us through. They think through all the possibilities that you may need. The food is outstanding. It was really lovely.
One thing worth noting regarding the recent travel concerns in the region - Shela (and the Peponi) are really well located and the area is well patrolled: by the military, Kenyan police and private security at the hotels, etc. Surprisingly, you don't really notice it (ie you don't feel like you're in some sort of police state), but it also feels very safe.
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