There are two ways to define bond order. The most technical definition of bond order is 1/2 * (# of electrons in bonding orbitals - # of electrons in antibonding orbitals), but this definition requires knowledge of molecular orbital theory to interpret.
The more simple definition is as you said, the number of bonds between a pair of atoms. For example, since the carbon in CO2 has a double bond to the oxygens, the bond order of the C-O bond in carbon dioxide is 2. Now, with NO3-, you are forgetting about resonance structures. Remember that no one resonance structure correctly represents the molecule you are representing (in fact, resonance structures do not exist in real life at all); rather, the molecule is most like an average of all the resonance structures of the molecule (i.e. a resonance hybrid). So, to find the bond order of NO3-, I would draw out all of the resonance structures (hint: there are three), then come up with the average number of bonds between the N and a specific O.