Certain government fee rules can depend on employer size or nonprofit status, but there is no universal small-business L-1B discount. Confirm the definitions and current charges for the actual petitioner and filing.
Price the complete case
A small employer may spend more preparation time assembling records that a larger organisation already maintains. Separate that work from government fees, any applicable supplemental charges, optional premium processing and family applications. Do not use company revenue alone to assume a fee category, and keep operating capital distinct from the immigration budget.
Filing fees are set by the filing rather than by the employer's size, though some charges depend on an employer's characteristics and should be verified against the actual petitioner rather than assumed. The cost that varies with size is preparation, and it often runs higher for a small company rather than lower, because the records that a larger organization produces as a matter of course have to be assembled from scratch. Expect time to be spent locating employment documentation, reconstructing what the employee actually did, and putting the corporate relationship on a documented footing.
Ask the adviser to identify which of that work is unavoidable and which depends on what the company can produce, and treat any quote given before anyone has looked at the records as provisional.