Hey Ritika, For nice hotels book at OYO. For cheap accommodation book zostels or hostels at www.hostelworld.com. In Allepay, you can spend one night at Backwaters houseboat but that would be little costly. Happy travelling!!!!!
Try zostel in Aleppey. They charge 500 per bed and the ambience there is awesome. Friendly strangers and cool interior, zostel is the best place to stay. For Munnar, try Goibibo, they offer the cheapest price.
I know I am few years late. But some luxury and cozy places to stay will be Ragamaya resort which is far from Munnar, just to relax and enjoy the view it is great. If you have to roam in and around in Munnar can stay at Chandys Windy woods. If you are planning for Suryanelli then better take Club Mahindra