Sounds like she's adjusting to the new baby. If she's crying and whining about something that you know she can explain to you in words, I would just make a habit of saying something like "My ears don't understand you, please use words to tell me what you need."
Also, if she's acting sad, acknowledge her feelings. Rather than tell her not to be sad, or to stop crying, say something like, "I can see you're upset about something. I'll be happy to listen when you can use words to speak to me." Maybe even offer her a little break for some rest while she collects herself -- "Would you like to sit in your room a while until you calm down, or sit on the couch?"
And, I think some "mommy time" or mommy dates are in order. With a 3-month old, you're probably coming out of the fog and extreme exhaustion from having a newborn, so maybe you can pick a time when the baby is napping for designated "mommy time" with your daughter. Play a game (Go Fish or Candy Land are great!), read books, paint/draw, bake cookies together...anything where you two can spend time together in a "big girl" way.
Mommy dates can be simple outings for just the two of you. Some things I've done with my daughter: Go on a walk or to a park, go to QT and get a fun drink from the soda fountains, go to an ice cream shop, trip to the library, a "girls" shopping trip when she needs new shoes or clothes, going to garage sales.
She just needs to feel like she's still in the picture, and needs a little attention. It doesn't mean that all whining will go away (does it EVER?), but it may solve a lot of it. I know that when my 4 yr old seems especially needy, if I take 20 minutes to play a game of candy land with her while her brother is napping, she feels "filled up" and will then be more content and play happily on her own the rest of the day.