If you wan to save cost.. of course malaysia stay in their hotel will be must more easier to go there plus cheaper accommodating. If you stay in singapore just wan to go legoland... also can.. but if you are going to visit that place alone.. why don just stay in malaysia.
if can afford, why not staying in spore and travel to legoland from spore....heard that is very near the second link (between spore and msia). After visiting legoland, can continue your fun in Universal Studio Spore.....not a bad idea to visit two theme parks...one stone kills two birds...
if enough budget, can plan stay in Singapore. But if want to stay JB also can, try to find more good facilities hotel. Because JB sure is more convenience compare to Singapore.