Greetings from Southeast Asia, and welcome to ScubaBoard!
Are you saying that you don't want to return to Malaysia? I would recommend that you consider more Malaysia diving before you embark on a trip to Lembeh. You could go up to the Perhentians or Redang, for example. Both of those have nice reefs which are great for inexperienced divers. Alternatively, you could go to the Sipadan area, also in Malaysia, but off the coast of Borneo. There are some great mid-priced dive resorts there, and at that time of year would be in the dry season.
Lembeh is wonderful, but I would recommend that you save this destination until you're a bit more experienced. Lembeh is special in that it's what we call "muck" diving. In other words, the dive sites are in areas that are not known for coral reefs but rather for silty bottoms, and the stuff you see is small, so you need to be quite close to the bottom to see these animals. Unless all three of you have developed outstanding buoyancy control (which generally takes quite a number of dives), dive in perfect trim, and have developed the habit of doing frog kicks while you dive, you are likely to kick up clouds of silt while you're diving, which means you won't see anything anyway, and other divers will wish you weren't around.
If you are interested in North Sulawesi, I would suggest considering Bunaken instead of Lembeh. Some resorts have branches both at Bunaken and at Lembeh, but the (very enjoyable) Black Sand resort is Lembeh only (yes, I have stayed to both Bunaken and Lembeh--including at Black Sand--and I have sent my divers to both as well).
In June, if you're sure you don't want to return to Malaysia, I'd strongly recommend Bali to you, specifically the Tulamben area. There is a great variety of diving there, with a shallow wreck, some walls, patchy reefs, and plenty of unusual critters along with some bigger stuff like bumphead parrotfish. Another option would be somewhere in the Philippines.