Slice tomatoes and jalapenos lengthwise. Remove skin from onion, halve and slice into 1/2 inch pieces.
Place tomatoes and jalapenos skin side up on a baking sheet with onion pieces and garlic. Place baking tray under broiler and cook for 6-8 minutes until charred. Remove from oven and allow to cool slightly.
Grill Method: Set grill to High (450°F). Oil grill basket or grill pan and spread whole tomatoes, jalapeños, halved onion and garlic. Grill until charred, turning to get both sides (5 to 10 minutes total depending on size).
In a blender or food processor, blend with chipotle pepper until smooth. Season with juice from one lime and salt to taste.
Chill covered until ready to serve with tortilla chips.