Yes, Monterosso is absolutely a good choice (it's my favourite, so I'm somewhat biased). It's the largest town and therefore has the greatest number of hotels, restaurants and other tourist amenities, as well as the best beaches. However, it's getting a bit late to get a booking for June, as many places will already be fully booked. See what you can find, and if you need other suggestions, post another note here.
Regarding "breaking up the journey" between Lucerne and the Cinque Terre, my preference would be to crack on and make the trip in one day. While that's a bit of a longer trip (~8 hours), my preference would be to spend the time enjoying Monterosso and the Cinque Terre, rather than wasting a night somewhere else. There's a train departing Lucerne at 09:18, arriving Monterosso at 17:05 (time 7H:47M, 2 changes), which is probably the one I'd use. That's a good time to arrive as you can check-in to your hotel and then go out for a fine meal in one of the restaurants, perhaps one with a patio overlooking the ocean.