Goa is undoubtedly favourite of all couples..Kerala is no less
Looking for mountains can go to sikkim..
MANALI is another good option considering weather as beaches might witness rainfall..check my blog on Manali and snowycastle..you’ll get the fair idea..HAPPY TRAVELLING
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You are a couple, so I'd suggest you go to some not-very-crowded places like Dharamshal, Manali or even Kashmir. Go to Chitkul. It is nice small place and has such great aura. You'd find Baspa river flowing where people would not go down and pollute it. Silence, sounds of nature and great camps (IBEX Camps, Look it up). It is a season for Chitkul, but still you would not find much crowd like other generic places. You can reach there by buses from Shimla, Chandigarh, taxi or even bike (Take the bike). Make your honeymoon special and explore the silence at Chitkul!